Dear all,
I have used ShapeIT to phase several VCF files. Each vcf file corresponding to a chromosome since ShapeIT can only phase when the data is separated by chromosome.
I now have outputted phased data for each chromosome as such trypanosome_chr1.phase, trypanosome_chr2.phase, etc.
I am wondering if there is now a way to merge these phased files together and have one .phase file that contains data for all chromosomes!
I hope this makes sense!!
Thank you very kindly any help would be greatly appreciated!
NG
•
written
by
nataliagru1
1 answer
If your downstream program (like RFMix) also processes each chromosome separately, perhaps you want to wait on the merging step.
I might have had other reasons to want to use a custom script to parse / join / filter .vcf files, but perhaps you could give vcftools a try?
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